Question

Any Simple Script To Calculate Fst Value Between Populations From Genomewide Snp Data (Available In Plink Format)

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13.5 years ago

User 0422 ▴ 150

Hi All,

I am looking for a simple script which calculate the fst between different populations, taking input as PLINK files (either ped or bed).

Thanks

snp ped bed fst plink • 17k views

ADD COMMENT • link updated 13.5 years ago by Davy ▴ 210 • written 13.5 years ago by User 0422 ▴ 150

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I'm surprised this hasn't been answered yet... want it too!

ADD REPLY • link 13.2 years ago by pufferfish ▴ 290

score 2 · Answer 1 · 2011-11-01

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13.1 years ago

Zach Stednick ▴ 660

Why not just use an existing program such as Genepop and write your own script to generate input files? Genepop provides plenty of example input files and once you have input your data it runs very fast.

ADD COMMENT • link 13.1 years ago by Zach Stednick ▴ 660

score 1 · Answer 2 · 2011-11-01

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13.1 years ago

Larry_Parnell 16k

Because Fst calculations are so much less complicated than iHS, we take a very programmatic approach to Fst calculations for our SNP panels. We have written a program to do this in a high-throughput manner. My colleague wrote a script in R or Perl, but this is so simple that it could even be done in Excel.

ADD COMMENT • link 13.1 years ago by Larry_Parnell 16k

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I'm looking to do some quick Fst calculations for a single SNP. I will use excel or a simple R script. I am looking for a good reference to an equation to calculate pair-wise Fst...

ADD REPLY • link 10.2 years ago by Scott ▴ 110

score 1 · Answer 3 · 2012-03-12

The R package hierfstat can do this. As well as computing Fst values, it can group your populations and compute Fst values for the groups. Very flexible. For in the input file I think plink ped files may need some reworking as it's been sometime since I've used it but the vignette can help you with that. Also has some cool functions for generating sample SNP data to vary mutation and migration rates and things like that.

Documentation here: http://cran.r-project.org/web/packages/hierfstat/hierfstat.pdf